title: RB vs. RN Replicate 1

city: Nanjing

first: JUN

last: HE

state: Jiangsu

address: Weigang 1

institute: Nanjing Agricultural University

description: Biological replicate 1 of 3

hyb_protocol: Each Cy5-labelled( 875 ng cRNA) was mixed with each of Cy3-labelled( 875 ng cRNA). The mixtures were applied to microarrays and hybridization was performed at 65°C for 17 h. After hybridization, slides were washed sequential

scan_protocol: Images were quantified using Agilent Feature Extraction Software(version 10.5.1.1)

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) with default setting was used for background subtraction and LOWESS normalization

source_name: resistant seedling pool infested with BPH for 24h

label_protocol: Two-color microarray analysis was performed with the Rice Expression 4x44K Microarray

growth_protocol: RH, 02428 and two rice pools (consisting of ten highly resistant or susceptible plants from an F2 population derived from a cross between the BPH-resistant rice cultivar Rathu Heenati (RH) and the susceptible cultivar 02428) were used for cDNA microarray assays. To ensure all seedlings were at the same growth stage for BPH infestation, seeds were pre-germinated in petri dishes. Seeds were sown in a 10 cm diameter plastic pot with a hole at the bottom.

extract_protocol: Total RNA were extracted using Trizol and were purified with QIAGEN RNeasy Mini Kit following manufacturer's instructions.

treatment_protocol: At the second-leaf stage, the seedlings were infested with 2nd to 3rd instar BPH nymphs at 10 insects per seedling.

value: seedling

value: 10 days

tag: phenotype

value: BPH-resistant

value: infested with BPH

source_name: resistant seedling pool without BPH infestation

value: without BPH infestation


title: RB vs. RN Replicate 2

status: Public on Nov 19 2019

type: RNA

country: China

description: Biological replicate 2 of 3

molecule: total RNA

organism: Oryza sativa

tag: tissue

tag: age

tag: treatment


title: RB vs. RN Replicate 3

description: Biological replicate 3 of 3


title: Untreated_Cells_1

type: SRA

city: Edinburgh

first: Julie

last: Rodor

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: UNIVERSITY OF EDINBURGH

library_source: transcriptomic

data_processing:
Fastq files were obtained from BGI
Gene quantification (read count and normalised expression value as FPKM) was obtained using RSEM 1.3.0 (options: -bowtie2 -forward-prob 0 -paired-end), based on GENCODE annotation version 25 (primary assembly).
Adapter and low quality sequences were removed using TrimGalore. Mapping was done using STAR based on GENCODE primary assembly GRCh38 genome and transcriptome version 26. Gene quantification was done using HTseq-count.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file with raw read count obtained by HTseq-count

organism: Homo sapiens

source_name: HPASMC

growth_protocol: Cultures of HPASMCs have been described previously (Deng et al, 2015. Circulation research). The culture was done using FBS depleted of EVs by overnight ultracentrifugation at 100,000·g.

extract_protocol:
RNA from HPASMCs and EVs was extracted with miRNeasy kit (Qiagen), quantified using Qubit technology and quality checked with the Agilent Bioanalyzer. The total amount of RNA obtained from EVs was 9 ng, thus we utilised a low-input RNA-Seq approach.
Library preparation was done with SMARTer Low-Input Strand-Specific Total RNASeq for Illumina and sequenced on a HiSeq 4000 by BGI Tech

treatment_protocol: Stimulation of HPASMCs was performed with TGF-β1 (10 ng/ml) or BMP4 (10 ng/ml) for 48h renewing stimuli every 24 h. For the Isolation of EVs, supernatants were centrifuged at 2000·g for 10’ at 4°C to remove dead cells. Then EVs were isolated by means of two steps of ultracentrifugation at 100,000·g for 1h at 4°C. The EV population in this pellet was confirmed by Nano Tracking Analysis (NTA) and western blot analysis for CD63 (EV marker) and His3 (nuclear marker, negative control).

value: HPASMC

value: Untreated

tag: rna source (evs/cells)

value: Cells

tag: replicate

value: replicate 1


title: RB vs. SB Replicate 3

description: Biological replicate 3 of 3

source_name: susceptible seedling pool infested with BPH for 24h

value: BPH-susceptible


title: 3BMB_18

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

source_name: lung biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

growth_protocol: All human lung biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

value: lung


title: RB vs. SB Replicate 2

description: Biological replicate 2 of 3


title: 3BMB_144


title: 3BMB_45


title: BMP4_EV_2

value: EVs

value: replicate 2


title: 96678

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

country: USA

institute: University of Michigan

data_processing:
We used our in-house analysis pipeline to perform adapter trimming, quality control, and processing for the RNA-seq samples.
Reads were mapped to the reference genome (NCBI build 37) using STAR
Gene expression levels were measured by HTSeq using GENCODE v24 as the gene annotation database
Only genes with more than 1 read/sample on average were retained for analysis.
Genome_build: NCBI build 37
Supplementary_files_format_and_content: genes x samples raw count matrix

source_name: PBMC

extract_protocol:
Substrate-attached cells were dislodged by pipetting and combined with floating cells, and total RNA was isolated using a RNeasy plus mini kit (Qiagen, Germantown, MD).
Sequencing libraries were prepared from the RNA using the Takara SMARTer pico input mammalian stranded total RNA sequencing kit (Takara Bio USA, San Francisco, CA).
The libraries were sequenced on an Illumina NextSeq instrument using 75 cycles to obtain a normalized read depth of 15-20 million reads per sample

treatment_protocol: PBMCs were cultured for 7 days with CD3/CD28 Dynabeads in the presence or absence of spontaneous NETs or NETs formed with exposure to 5 ng/ml LPS.

tag: patientid

tag: condition

tag: traf3ip2 genotype


title: Untreated_EV_3

value: replicate 3


title: TGFb1_EV_1


title: 96677


title: 3BMB_77


title: Untreated_EV_2


title: 96676


title: 3BMB_50


title: 3BMB_16


title: 3BMB_189


title: RH vs. 02428 Replicate 2

description: Biological replicate 2 of 2

source_name: RH seedling after infestation with BPH for 24h

source_name: 02428 seedling after infestation with BPH for 24h


title: RB vs. SB Replicate 1

description: Biological replicate 1 of 3


title: RH vs. 02428 Replicate 1

description: Biological replicate 1 of 2


title: 96675


title: 96674

value: wt


title: 96671


title: 96672


title: 96670


title: 3BMB_132


title: 96669


title: Parental A431-5

city: Montreal

first: Anie

last: Philip

address: 1650 Cedar Avenue

institute: Mcgill university

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) 4.0.1 (TCA 4.0) using Clariom_S_Human.na36.hg38.transcript.csv

source_name: Human A431  cell line

label_protocol: Affymetrix

extract_protocol: Total RNA was isolated from cultured cells using RNeasy mini Kit (Cat. NO. 74104, QIAGEN)

treatment_protocol: Knockout CD109 by CRISPR/case9

tag: cell line

tag: genotype/variation

value: Wildtype


title: 3BMB_53


title: 3BMB_180


title: Parental A431-6


title: Parental A431-2


title: AS-naive-day12-rep1

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: iScan system, Illumina

data_processing: Detection pvalues were calculated from the idat files using Limma's detectionPvalues function within R.  Data were subsequently background corrected and quantile normalized using Limma's neqc function with default settings.

organism: Mus musculus

source_name: Mouse spleen

label_protocol: cRNA samples were prepared from total splenic RNA using Illumina TotalPrep RNA Amplification Kit (Ambion)

extract_protocol: Single cell suspensions were made in PBS, and Total splenic RNA was extracted using RiboPure Kit (Ambion) following the manufacturer's protocol

tag: strain

tag: gender

value: female

value: 6-8 weeks

value: spleen

tag: agent

value: naive

tag: day


title: CD109-KO-Clone32

source_name: Human A431 CD109-KO cell line


title: 3BMB_27


title: 3BMB_30


title: CD109-KO-Clone180


title: AS-infected-day12-rep4

value: Plasmodium chabaudi chabaudi AS (PcAS) infected


title: AS-infected-day12-rep2


title: Cardiomyocytes, High, 24 h, MS-180

city: Frederick

first: Patric

last: Schyman

state: Maryland

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute (BHSAI)

description: Treatment

data_processing:
RNA-seq data were analyzed using the Kallisto tool (version 0.42.4) for read alignment and quantification.
We calculate uncertainties of transcript abundance estimates by repeating the analyses 100 times after resampling with replacement. We pseudo-aligned the reads to the Rattus norvegicus transcriptome (Rnor_6.0) downloaded from the Ensembl website
Kallisto input: kallisto quant -i $REF_KAL2 -b 100 -o rat_Edik/"$sample"  $DATA_DIR/3744-"$sample"_R1_001.fastq.gz $DATA_DIR/3744-"$sample"_R2_001.fastq.gz -t 10
Genome_build: Rattus norvegicus transcriptome (Rnor_6.0)
Supplementary_files_format_and_content: tab-delimited text files, including abundance measurements

organism: Rattus norvegicus

source_name: Cardiomyocytes, High (1.50 mM)

growth_protocol: We cultured rat hepatocytes, renal cells, and cardiomyocytes for an additional 18 hours before adding thioacetamide-S-oxide or vehicle (maintenance medium; MM250 for hepatocytes and EpiCM for renal cells).

extract_protocol:
Total RNA was isolated from culture cells using TRIzol Reagent (Thermo Fisher Scientific, Waltham, MA) and the direct-zol RNA MiniPrep kit (Zymo Research, Irvine, CA). The isolated RNA samples were then submitted to the Vanderbilt University Medical Center VANTAGE Core (Nashville, TN) for RNA quality determination and sequencing. Total RNA quality was assessed using a 2100 Bioanalyzer (Agilent, Santa Clara, CA).
At least 200 ng of DNase-treated total RNA with high RNA integrity was used to generate poly-A-enriched mRNA libraries, using KAPA Stranded mRNA sample kits with indexed adaptors (New England BioLabs). Library quality was assessed using the 2100 Bioanalyzer (Agilent), and libraries were quantitated using KAPA library Quantification kits (KAPA Biosystems). Pooled libraries were subjected to 150-bp double-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq6000). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.

value: Sprague-Dawley Rat

value: Heart

tag: cell type

value: Cardiomyocytes

value: thioacetamide-S-oxide

tag: dose

value: High (1.50 mM)

tag: duration


title: AS-infected-day12-rep3

tag: tissue


title: AS-naive-day12-rep2

tag: age


title: Cardiomyocytes, High, 24 h, MS-179

description: Treatment


title: 3BMB_156


title: 3BMB_11


title: 3BMB_131


title: 96667


title: AS-infected-day10-rep3


title: Cardiomyocytes, High, 24 h, MS-178

description: Treatment


title: 96668


title: 96666


title: Cardiomyocytes, High, 24 h, MS-177

description: Treatment


title: 96665


title: 96664


title: 96663


title: CD109-KO-Clone26


title: Cardiomyocytes, Low, 24 h, MS-175

description: Treatment

source_name: Cardiomyocytes, Low (0.50 mM)


title: AS-infected-day10-rep1


title: Cardiomyocytes, Low, 24 h, MS-174

description: Treatment


title: 96662


title: AS-infected-day8-rep4


title: Cardiomyocytes, Low, 24 h, MS-173

description: Treatment


title: 3BMB_168


title: 96661


title: 3BMB_26


title: AS-naive-day12-rep3


title: AS-infected-day8-rep3


title: 3BMB_112


title: 3BMB_90


title: AS-infected-day8-rep1


title: Cardiomyocytes, Low, 24 h, MS-172

description: Treatment


title: AS-infected-day6-rep3


title: Cardiomyocytes, High, 24 h, MS-176

description: Treatment


title: AS-infected-day10-rep2


title: AS-infected-day6-rep4


title: Cardiomyocytes, Low, 24 h, MS-171

description: Treatment


title: 3BMB_187


title: 96659


title: 96660


title: 96658


title: AS-infected-day6-rep1


title: Cardiomyocytes, High, 9 h, MS-165

description: Treatment

value: 9 h


title: Cardiomyocytes, High, 9 h, MS-164

description: Treatment


title: Cardiomyocytes, High, 9 h, MS-163

description: Treatment


title: 96656


title: 96657


title: Cardiomyocytes, High, 9 h, MS-162

description: Treatment


title: 96655


title: AS-infected-day4-rep4


title: AS-infected-day6-rep2


title: 3BMB_28

value: lung


title: 3BMB_186


title: 3BMB_188


title: 3BMB_185


title: AS-infected-day4-rep3


title: AS-infected-day4-rep1


title: 96654


title: 96653


title: Cardiomyocytes, Low, 9 h, MS-160

description: Treatment


title: Cardiomyocytes, Low, 9 h, MS-159

description: Treatment


title: 96652


title: Cardiomyocytes, High, 9 h, MS-161

description: Treatment


title: 96651


title: Cardiomyocytes, Low, 9 h, MS-157

description: Treatment


title: Cardiomyocytes, Low, 9 h, MS-156

description: Treatment


title: Donor_41 cALL_RNS_63

city: Debrecen

first: Szilard

last: Poliska

address: Egyetem ter 1.

department: Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

description:
Donor_41
Gene expression data of peripheral blood mononuclear cells

hyb_protocol: Samples were hybridized at 45 degrees Celsius for 16 hours and then standard washing protocol was performed using GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned on GeneChip Scanner 7G (Affymetrix), Affymetrix GeneChip Command Console (AGCC) was used to obtain image files.

data_processing:
CHP files were generated using Affymetrix Expression Control.
Downstream data analysis was performed in GeneSpring GX 12,  CEL files were imported using RMA algorithm and median normalization was performed.

source_name: bone marrow

label_protocol: 3' IVT Expression Kit (Affymetrix) was used for amplifying and labeling 150 ng of RNA samples.

growth_protocol: Bone marrow samples of BCP-ALL patients  were collected into PAXgene Blood RNA Plastic Tube (PreAnaltyX, Hombrechtikon, Switzerland). Total cellular RNA was isolated using PAXgene Blood miRNA Kit (PreAnalityX) according to manufacturer's protocol.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Patients were treated according to BFM ALL-IC 2009 clinical trial (EuDraCT No)

value: male

tag: protein expression of fxiii-a

value: moderate

tag: genetic sub-type

value: non-B-other


title: Donor_40 cALL_RNS_62

description:
Donor_40
Gene expression data of peripheral blood mononuclear cells


title: Cardiomyocytes, Low, 9 h, MS-158

description: Treatment


title: AS-infected-day2-rep3

tag: replicate


title: Donor_42 cALL_RNS_64

description:
Donor_42
Gene expression data of peripheral blood mononuclear cells


title: AS-infected-day2-rep4


title: 96679

tag: patientid


title: AS-infected-day4-rep2


title: AS-infected-day2-rep2


title: Cardiomyocytes, Vehicle, 24 h, MS-170

description: Control

source_name: Cardiomyocytes, Vehicle

value: Control

value: Vehicle


title: Brain, F1252_F_HFD

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto Street

department: Enviromantal and Occupational health

institute: University of Pittsburgh

data_processing:
fastq to bam using subread v1.4.0
featurecounts usinge Rsubread v1.22.0
edgeR analysis using v3.14.0
Genome_build: mm9
Supplementary_files_format_and_content: Reads_ALL.xlsx (.x extension corresponds to CPM, and .y extension corresponds to raw reads)

source_name: brain

growth_protocol: All animal experiments were approved by the University of Pittsburgh Institutional Animal Care and Use Committee. All procedures were carried out in accordance with the approved guidelines. APP23 transgenic mice (C57Bl6 background) expressing human APP751 familial Swedish AD mutation (APPK670N, M671L) were crossed to wild-type C57BL/6 mice to generate APP23 hemizygous mice

extract_protocol:
Mice were anesthetized with Avertin (250 mg/kg of body weight, i.p.) and perfused transcardially with cold 0.1 M PBS, pH 7.4: left hemisphere fixed in 4% paraformaldehyde for histology. The cortex was dissected from the other and snap frozen on dry ice for RNA and protein isolation
RNA was isolated from cortex and purified using RNeasy mini kit (Qiagen) per the manufacturer’s protocol. RNA quality was assessed using 2100 Bioanalyzer (Agilent Technologies) and samples with RIN > 8 were further used for sequencing. Sequencing libraries were generated using mRNA Library Prep Reagent Set (Illumina) according to the manufacturer’s recommendations

treatment_protocol: Male and female APP23 mice (mean age 11.7 months) were randomly assigned to ND (Prolab Isopro RMH 3000, Lab Diet) or HFD (D12079B RD Western Diet, Research Diets). HFD supplemented 40% calories from fat; 16.8% from protein and 42.6% from carbohydrates. Fat was provided as anhydrous milk fat and corn oil. The mice had free access to water and food. After 3 months of feeding, behavior was assessed at mean age of 14.7 months.

tag: Sex

value: Female

tag: treatment

value: HFD

value: brain


title: Donor_38 cALL_RNS_60

description:
Donor_38
Gene expression data of peripheral blood mononuclear cells


title: Donor_37 cALL_RNS_59

description:
Donor_37
Gene expression data of peripheral blood mononuclear cells

value: female


title: Donor_39 cALL_RNS_61

description:
Donor_39
Gene expression data of peripheral blood mononuclear cells


title: Donor_36 cALL_RNS_58

description:
Donor_36
Gene expression data of peripheral blood mononuclear cells


title: 96648

tag: condition

tag: traf3ip2 genotype

value: wt


title: Donor_35 cALL_RNS_57

description:
Donor_35
Gene expression data of peripheral blood mononuclear cells

value: B-other


title: Brain, F1145_M_HFD

value: Male


title: AS-naive-day0-rep2

tag: strain

value: 6-8 weeks

value: spleen

value: naive


title: AS-naive-day0-rep3

tag: gender


title: AS-naive-day0-rep1

tag: agent


title: AS-infected-day2-rep1

value: Plasmodium chabaudi chabaudi AS (PcAS) infected

tag: day


title: Cardiomyocytes, Vehicle, 24 h, MS-169

description: Control

value: Sprague-Dawley Rat

value: Heart

tag: cell type

value: Cardiomyocytes


title: 96650


title: 96649


title: Brain, F1139_F_ND

value: ND


title: Cardiomyocytes, Vehicle, 24 h, MS-168

description: Control

value: Control

tag: dose


title: Donor_33 cALL_RNS_55

description:
Donor_33
Gene expression data of peripheral blood mononuclear cells

value: moderate


title: 96647


title: 96645


title: Cardiomyocytes, Vehicle, 24 h, MS-167

description: Control

value: Vehicle

tag: duration


title: 96644


title: Brain, F1129_M_HFD

value: HFD

tag: tissue


title: Cardiomyocytes, Vehicle, 24 h, MS-166

description: Control


title: Brain, F1128_M_ND

value: brain


title: Donor_32 cALL_RNS_54

description:
Donor_32
Gene expression data of peripheral blood mononuclear cells

value: female

tag: age

value: negative


title: 96641

value: wt


title: Brain, F1102_F_ND

value: Female


title: Brain, F1104_F_ND


title: Cardiomyocytes, Vehicle, 9 h, MS-155

description: Control

value: 9 h


title: Cardiomyocytes, Vehicle, 9 h, MS-154

description: Control


title: 96642


title: Donor_29 cALL_RNS_51

description:
Donor_29
Gene expression data of peripheral blood mononuclear cells

tag: protein expression of fxiii-a

value: B-other


title: 96640


title: Donor_31 cALL_RNS_53

description:
Donor_31
Gene expression data of peripheral blood mononuclear cells

value: male

tag: genetic sub-type


title: Donor_34 cALL_RNS_56

description:
Donor_34
Gene expression data of peripheral blood mononuclear cells


title: Cardiomyocytes, Vehicle, 9 h, MS-153

description: Control


title: Donor_30 cALL_RNS_52

description:
Donor_30
Gene expression data of peripheral blood mononuclear cells


title: Donor_27 cALL_RNS_49

description:
Donor_27
Gene expression data of peripheral blood mononuclear cells


title: 96639


title: Cardiomyocytes, Vehicle, 9 h, MS-152

description: Control


title: Brain, F1131_M_ND

value: Male


title: Brain, F1100_F_HFD


title: Brain, F1094_F_HFD


title: Cardiomyocytes, Vehicle, 9 h, MS-151

description: Control

value: Sprague-Dawley Rat


title: Donor_28 cALL_RNS_50

description:
Donor_28
Gene expression data of peripheral blood mononuclear cells


title: 96638


title: 96643


title: Brain, F1080_M_ND


title: 96637


title: Renal tube epithelial cells, High, 24 h, MS-150

description: Treatment

source_name: Renal tube epithelial cells, High (0.500 mM)

value: Kidney

value: Renal tube epithelial cells

value: thioacetamide-S-oxide


title: Donor_26 cALL_RNS_47

description:
Donor_26
Gene expression data of peripheral blood mononuclear cells

value: non-B-other


title: Donor_24 cALL_RNS_45

description:
Donor_24
Gene expression data of peripheral blood mononuclear cells

value: moderate


title: Donor_25 cALL_RNS_46

description:
Donor_25
Gene expression data of peripheral blood mononuclear cells


title: Renal tube epithelial cells, High, 24 h, MS-149

description: Treatment


title: Brain, F1076_F_HFD


title: Renal tube epithelial cells, High, 24 h, MS-148

description: Treatment


title: 96636


title: Control S. sonnei culture 3

first: Vincenzo

last: Torraca

state: London

address: Keppel street

institute: LSHTM

data_processing:
Base-calling was perform online during the sequencing procedure with the Real-Time Analysis (RTA) software version 2.4.11 and System Suite Version 2.1.2.1.
Conversion of the bcl2 file to de-multiplexed gzipped fastq files was performed using the bcl2fastq script v. 2.18.0.12 provided by Illumina.
Quality and adapter trimming of fastq files was performed with trimmomatic-0.36.jar SE using parameters: -phred33;ILLUMINACLIP:adapter:2:30:10;SLIDINGWINDOW:4:15;LEADING:3;TRAILING:3;MINLEN:30
Mapping of the reads to the genomes was performed with bowtie2 using parameter --local
Read counting was performed with featureCounts version 1.5.0-p1
Genome_build: GRCz11 (Danio rerio), ASM28371v1  (S. sonnei 53G)
Supplementary_files_format_and_content: tab-separated values (TSV) files include geneID, gene name, gene description, log2foldchange (Deseq2), pvalue (Deseq2), padj (Deseq2), chromosome name, position (start, end and strand), length, reads and RPKM per each sample

organism: Shigella sonnei

source_name: S. sonnei culture

growth_protocol: Bacteria were firsts grown at 37C O/N from glycerol stocks on tryptic soy agar plates containing 0.01% Congo red and 100 ug/ml Carbenicillin. One single smooth colony accumulating Congo red was selected and cultured O/N in tryptic soy broth containing 100 ug/ml Carbenicillin  at 37C with agitation. O/N culture was then diluted 50x in tryptic soy broth containing 25 ug/ml Carbenicillin and grown at 37C with agitation until culture reached an OD of 0.55-0.65 at 600 nm. Bacteria for control cultures were then diluted 50x and incubated at 28.5C in a total of 5 ml until they reached an OD of 0.55-0.65. The remaining of the original culture was instead spun down and further processed for injections. (see S. sonnei infected larvae sample)

extract_protocol:
Samples were snap frozen at -80°C, then 100 μl of RNA protect bacteria reagent (Qiagen) was added, followed by mechanical trituration with a pestle blender. Samples were supplemented with 100 μl of 30 mM Tris-HCl/1 mM EDTA solution at pH = 8, 33 μl of 50 mg/ml lysozyme (Thermo Scientific), 33 μl of proteinase K >600 U/ml (Thermo Scientific) and shaken for 20 min RT. Lysis was completed by adding 700 μl of RTL buffer (Qiagen), 3 μl of 1 M dithiothreitol (Sigma-Aldrich) and mechanical disruption. Undigested debris were spun down 3 min 10000 rpm and the supernatant was supplemented with 500 μl of 100% ethanol prior loading onto RNeasy mini columns (Qiagen). From this step onwards, the manufacturer’s guidelines were followed for RNA purification. RNA quality and integrity were assessed by using NanoDrop and Non-denaturing agarose gel electrophoresis. For further quality check, RNA sequencing, library construction and reads count, samples were outsourced to Vertis Biotechnologie AG (Freising, Germany). Bacterial and host mRNA were enriched prior library preparation by using Ribo-Zero Gold rRNA Removal Kit (Epidemiology, Illumina, San Diego, California).
The rRNA depleted RNA samples were first fragmented using ultrasound (4 pulses of 30 s each at 4°C). Then, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase . The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). For Illumina NextSeq sequencing, the samples were pooled in approximately equimolar amounts. The cDNA pool was size fractionated in the size range of 200 – 550 bp using a preparative agarose gel. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina. The cDNA pools were sequenced on an Illumina NextSeq 500 system using 75 bp read length.

value: 53G transformed with pFPV25.1

tag: incubation temperature

tag: collection point

value: OD reached 0.6


title: 96635

tag: patientid


title: Brain, F1074_F_ND

tag: Sex

tag: treatment

value: ND

value: brain


title: Brain, F1073_F_ND


title: Renal tube epithelial cells, High, 24 h, MS-147

description: Treatment


title: Control S. sonnei culture 2

description: ssonnei_processed_data.tsv, zebrafish_processed_data.tsv


title: Brain, F1065_M_HFD

value: HFD


title: Renal tube epithelial cells, High, 24 h, MS-146

description: Treatment


title: Control S. sonnei culture 1


title: Renal tube epithelial cells, Low, 24 h, MS-144

description: Treatment

source_name: Renal tube epithelial cells, Low (0.125 mM)


title: Renal tube epithelial cells, Low, 24 h, MS-145

description: Treatment


title: Brain, F1063_F_HFD


title: Brain, F1079_M_ND


title: Npun_F1710/11 overexpresser rep3

city: Tucson

first: Kerry

middle: Kevin

last: Cooper

state: AZ

address: 1117 E. Lowell St.

department: School of Animal and Comparative Biomedical Sciences

institute: University of Arizona

description:
High levels of alkane production
cuffdiff_gene_exp.diff.txt

data_processing:
Each sample’s reads were aligned to the N. punctiforme complete genome sequence (Genbank accession number: CP001037) using Tophat software (v2.0.13; http://ccb.jhu.edu/software/tophat/fusion_index.shtml), and expression levels were quantified using Cufflinks software (v2.2.1). Finally, all the individual Cufflink outputs were merged together using Cuffmerge software (v1.0.0), and the WTC transcriptome was compared to the LD/alkane overproducer (2g) transcriptome using Cuffdiff software (v2.2.1). The output provided significant differences (q-value <0.05) between the WTC and 2g strains based on Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
Genome_build: N. punctiforme complete genome sequence (Genbank accession number: CP001037)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample; normalized abundance measurements output from Cuffdiff

organism: Nostoc punctiforme PCC 73102

source_name: Bacterial culture

growth_protocol: Nostoc punctiforme PCC 73102 (ATCC 29133) liquid cultures were grown in 125 mL Erlenmeyer flasks containing 50 mL of Allen and Arnon media (AA) diluted four-fold (AA/4) (Allen and Arnon, 1955) supplemented with 5 mM 3-(N-morpholino)propanesulfonic acid (MOPS), 2.5 mM NH4Cl, 2.5 mM KNO3 and 2.5 mM NaNO3 (collectively known as MAN). Plate AA media was not diluted and contained MAN and 1% Noble agar. Cultures harboring plasmid, pSCR119, were supplemented with neomycin at a final concentration of 10 μg/mL. Flasks were incubated under a white fluorescent light (12–15 μmol photons/m2/sec) at 25 °C and shaken at 120 rpm. Plates were incubated at the same illumination and temperature without shaking in a CO2 enriched (5,000 ppm) growth chamber.

extract_protocol:
Triplicate cultures of log phase wild-type plasmid-only control (WTC) and 2g strains were harvested by a 2-minute centrifugation at 6,000xg. The pellet was suspended in 700 µl of media prior to flash freezing and storage at -80°C. RNA was harvested as previously described {Schmidt-Goff, 1993 #1370}. The samples were then further purified using a RNeasy Mini Kit (Qiagen) with on-column DNase treatment. Samples were aliquoted and stored at -80°C until used. 5 µg of each sample were cleaned and concentrated further using an RNA Clean & Concentrator -5 kit (Zymo). rRNA depletion was then performed using Terminator 5’-Phosphate-Dependent Exonuclease (Epicentre) following the manufacturer’s protocol using Buffer A
RNA libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina per the manufacturer’s instructions. To determine the quality of the libraries, an Experion 1K DNA analysis kit (Bio-Rad) was used to assess the size distribution of the cDNA library following manufacturer’s instructions. Each cDNA library was quantified using a Qubit Fluorometer and Qubit dsDNA High Sensitivity reagents (Invitrogen) using manufacturer’s instructions, and also using qPCR following the protocol from the Library Quantification Kit for Illumina platforms (KAPA cat # 0796014000). Samples were normalized to 10 nM and multiplexed based on qPCR derived concentrations. The multiplexed library containing all 6 samples were sequenced on an Illumina HiSeq 2500 system where 100 bp single-end reads were generated (UC Irvine Genomics High Throughput Facility).

treatment_protocol: The two gene Npun_F1710/11 expression (2g) plasmid was made by PCR amplifying adjacent genes Npun_R1711 and Npun_R1710 and the upstream intergenic region with subsequent cloning into pSCR119, a shuttle plasmid capable of replication in both E. coli and N. punctiforme as previously described (Peramuna, 2015).

tag: alkane production

value: Higher than normal


title: Renal tube epithelial cells, Low, 24 h, MS-143

description: Treatment

tag: strain


title: 3BMB_111

value: lung


title: Npun_F1710/11 overexpresser rep2


title: Donor_23 cALL_RNS_44

description:
Donor_23
Gene expression data of peripheral blood mononuclear cells

tag: gender


title: Donor_20 cALL_RNS_35

description:
Donor_20
Gene expression data of peripheral blood mononuclear cells

value: negative


title: Donor_21 cALL_RNS_36

description:
Donor_21
Gene expression data of peripheral blood mononuclear cells

value: female


title: Donor_19 cALL_RNS_34

description:
Donor_19
Gene expression data of peripheral blood mononuclear cells

value: B-other


title: Npun_F1710/11 overexpresser rep1


title: Donor_18 cALL_RNS_33

description:
Donor_18
Gene expression data of peripheral blood mononuclear cells


title: Renal tube epithelial cells, Low, 24 h, MS-142

description: Treatment

tag: agent


title: Donor_17 cALL_RNS_26

description:
Donor_17
Gene expression data of peripheral blood mononuclear cells

value: male


title: Donor_22 cALL_RNS_37

description:
Donor_22
Gene expression data of peripheral blood mononuclear cells

value: positive


title: Renal tube epithelial cells, Low, 24 h, MS-141

description: Treatment

value: Sprague-Dawley Rat

value: Kidney


title: Donor_16 cALL_RNS_19

description:
Donor_16
Gene expression data of peripheral blood mononuclear cells


title: HD_IgG

city: Berlin

first: Ferah

last: Yildirim

address: Charitéplatz 1, Virchowweg 6

country: Germany

institute: Charité Berlin

library_source: genomic

data_processing:
Raw ChIP-seq data were processed using the Illumina software pipeline. ChIP-seq reads were aligned to the reference mouse genome (mm9; UCSC) using Bowtie.
Binding events were identified using the GPS (genome positioning system) and MACS (model-based analysis of ChIP-seq) algorithms.
IgG-bound DNA libraries were used as the control. Genes associated with binding events inferred from ChIPseq were identified using annotations from the refFlat (RefSeq database) file from the UCSC mm9 tables.
For visualization of read density at specific loci, ChIP-seq aligned reads were shifted according to a peak shift model built by MACS and uploaded to the UCSC genome browser.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.bw: bigWig files for visualization of read density at specific loci, ChIP-seq aligned reads were shifted according to a peak shift model built by MACS and uploaded to the UCSC genome browser.

molecule: genomic DNA

source_name: striatum

extract_protocol:
Crosslinked tissues were fragmented to the size range of 100–500 bp using a Bioruptor (Bioruptor Next Gen; Diagenode). Antibodies that specifically recognizes H3K27 acetylation (Abcam, ab4729) and Elk-1 protein (Santa Cruz, sc-355X) along with nonspecific rabbit IgG (Millipore, 17-614) were incubated with beads for 6 h before incubating with sonicated chromatin overnight.
Immunoprecipitated DNA and nonspecific IgG-bound DNA were prepared for high-throughput sequencing according to Illumina's instructions and sequenced on an Illumina platform following the manufacturer’s standard protocol.

tag: model

value: R6/1 and CHL2

value: Striatum

tag: chip antibody

value: Rabbit IgG (Millipore, 17-614)


title: WT_IgG


title: WT rep3

description:
Control strain
cuffdiff_gene_exp.diff.txt

value: Normal


title: WT rep2


title: Renal tube epithelial cells, High, 9 h, MS-134

description: Treatment

tag: cell type

value: Renal tube epithelial cells

value: thioacetamide-S-oxide

tag: dose

value: 9 h


title: Renal tube epithelial cells, High, 9 h, MS-135

description: Treatment

tag: tissue

tag: duration


title: CHL2_rep1_2_3 [CHL2]

tag: age

value: 1 year

value: H3K27 acetylation (Abcam, ab4729)


title: WT rep1


title: Donor_15 cALL_RNS_18

description:
Donor_15
Gene expression data of peripheral blood mononuclear cells

tag: protein expression of fxiii-a

tag: genetic sub-type

value: non-B-other


title: Brain, A1095_M_HFD

value: Male

value: HFD

value: brain


title: WT_rep1_2_3 [CHL2]


title: Renal tube epithelial cells, High, 9 h, MS-133

description: Treatment


title: Brain, A1092_F_ND

value: Female

value: ND


title: Donor_14 cALL_RNS_17

description:
Donor_14
Gene expression data of peripheral blood mononuclear cells

value: female

value: negative


title: Donor_13 cALL_RNS_16

description:
Donor_13
Gene expression data of peripheral blood mononuclear cells

value: male

value: B-other


title: R61_rep1_2_3 [R6/1]

value: 8 weeks

value: Striatum

value: Elk-1 (Santa Cruz, sc-355X)


title: Donor_12 cALL_RNS_15

description:
Donor_12
Gene expression data of peripheral blood mononuclear cells


title: P5_25h_C

city: Oeiras

first: Cecilia

middle: M.

last: Arraiano

address: Av. Republica, Apt 127

country: Portugal

institute: Instituto de Tecnologia Quimica e Biologica (ITQB) / Univ. Nova de Lisboa

data_processing:
The quality of the RNA-Seq data was confirmed using fastQC program. Contaminant adapters and low quality reads were removed with cutadapt and the remaining reads were mapped against P. putida genome (NC_002947.4, downloaded from NCBI genome database) using Bowtie2 program. More than 90% of all reads were uniquely aligned. Samtools was used to sort the mapping files by genomic position.
Detection of novel putative sRNAs was performed with the sRNA-Detect program and the genome browser Artemis. Quantification of reads was accomplished with featureCounts and normalization of the expression levels was achieved with the Reads Per Kilobase Million (RPKM) method.
Genome_build: NC_002947.4
Supplementary_files_format_and_content: tab-delimited text file include novel predicted ncRNAs and RPKM values for each condition

organism: Pseudomonas putida

source_name: Culture cells

growth_protocol: Bioreactor cultivations were carried out with a minimal medium containing (per liter) 13.14 g glucose, 1.00 g NaH2PO4·2H2O, 2.6 g K2HPO4, 9 g (NH4)2SO4, and trace element solution with the same composition as that used in the shaking flask minimal medium. One hundred and fifty milliliters of preculture was used as the inoculum. Cultivations were started with an initial volume of VSTR=1.5 L at a total pressure of 1.5 bar in a 3 L bioreactor at 37 °C (Bioengineering, Wald, Switzerland) with a six-blade Rushton type impeller (constant Power input of 5 W) and constant aeration rate (1.5 L min−1).

extract_protocol:
RNA was isolated following cell lysis and phenol:chloroform extraction as described in SOP (doi:10.15490/fairdomhub.1.sop.285.4)
Total RNA was sent to Stabvida for sequencing (Illumina, paired-end, 150bp, 20M reads). rRNA was depleted from the samples with the RiboZero kit and sequencing libraries were constructed with the TrueSeq kit for bacteria from Illumina.

tag: growth condition

value: Bioreactor with low glucose content

tag: genotype

value: Wild-type


title: P3_25h_C


title: P1_25h_C


title: Renal tube epithelial cells, High, 9 h, MS-131

description: Treatment

value: Sprague-Dawley Rat

value: Kidney

value: Renal tube epithelial cells

value: thioacetamide-S-oxide

value: 9 h


title: R61_rep1_2_3_4 [R6/1]

value: H3K27 acetylation (Abcam, ab4729)


title: WT_rep1_2_3 [R6/1]


title: Donor_11 cALL_RNS_14

description:
Donor_11
Gene expression data of peripheral blood mononuclear cells


title: Renal tube epithelial cells, Low, 9 h, MS-130

description: Treatment


title: WT_rep1_2_3_4 [R6/1]


title: Renal tube epithelial cells, Low, 9 h, MS-129

description: Treatment


title: S_9h_C


title: Renal tube epithelial cells, Low, 9 h, MS-128

description: Treatment


title: S_3h_C


title: Renal tube epithelial cells, Low, 9 h, MS-127

description: Treatment


title: Renal tube epithelial cells, High, 9 h, MS-132

description: Treatment


title: P5_15min_C


title: Renal tube epithelial cells, Vehicle, 24 h, MS-140

description: Control

source_name: Renal tube epithelial cells, Vehicle

value: Control

value: Vehicle


title: Elk-1_AAV_R6/1_rep3

description: processed data file: RNAseq__Elk1_AAV__processed_ctrl_AAV_R6-1_vs_Elk1_AAV_R6-1_All_exp_f0.1.txt

data_processing:
After sequencing, the raw paired-end reads of the cDNA fragments were aligned to the mouse (RefSeq, mm9) transcriptome using a spliced junction discovery tool, TopHat, and short-read alignment tool, Bowtie.
Differential expression across the biological replicates in each condition were called using the Cufflinks algorithm with bias and multi-read correction options. Reads mapping to rRNA and mitochondrial transcripts were masked.
Genes meeting a minimum threshold of 0.1 FPKM in at least one of the conditions were tested for differential expression and used as a background for functional enrichment of differentially expressed genes in Gorilla.
Pairwise log2 fold changes in expression were calculated from the FPKM levels at every gene after pseudocounts of 0.05 FPKM were added to every gene to mitigate inflated fold changes at poorly expressed genes.
Genes were called differentially expressed if the p-value was less than 0.05 after multiple hypothesis correction and the absolute log fold change was greater than 0.5.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files contain cuffdiff output with columns: (1) tested id, (2) gene, (3) locus, (4) sample 1, (5) sample 2, (6) test status, (7) FPKM of the gene in sample 1, (8) FPKM of the gene in sample 2, (9) log2(FPKM_2/FPKM_1), (10) test statistic, (11) p-value, (12) q-value, (13) significant (yes or no). See http://cole-trapnell-lab.github.io/cufflinks/manual/ for more details.

extract_protocol:
Brain tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

value: 10 weeks


title: S_25h_C


title: Elk-1_AAV_R6/1_rep2


title: Elk-1_AAV_R6/1_rep1


title: Donor_10 cALL_RNS_13

description:
Donor_10
Gene expression data of peripheral blood mononuclear cells

value: negative

value: non-B-other


title: Elk-1_AAV_R6/1_rep4


title: P3_15min_C


title: Donor_6 cALL_RNS_06

description:
Donor_6
Gene expression data of peripheral blood mononuclear cells

value: female

value: positive


title: Donor_8 cALL_RNS_08

description:
Donor_8
Gene expression data of peripheral blood mononuclear cells


title: Renal tube epithelial cells, Vehicle, 24 h, MS-139

description: Control


title: Donor_7 cALL_RNS_07

description:
Donor_7
Gene expression data of peripheral blood mononuclear cells


title: ctrl_AAV_R6/1_rep1

description: processed data file: RNAseq__Elk1_AAV__processed_R6-1_vs_WT_exp_f0.1.txt

value: Striatum


title: Donor_5 cALL_RNS_05

description:
Donor_5
Gene expression data of peripheral blood mononuclear cells


title: Renal tube epithelial cells, Vehicle, 24 h, MS-138

description: Control


title: Donor_4 cALL_RNS_04

description:
Donor_4
Gene expression data of peripheral blood mononuclear cells

value: moderate


title: ctrl_AAV_WT_rep2


title: Donor_3 cALL_RNS_03

description:
Donor_3
Gene expression data of peripheral blood mononuclear cells


title: S_1h_C

value: Bioreactor with low glucose content


title: Renal tube epithelial cells, Low, 9 h, MS-126

description: Treatment


title: Renal tube epithelial cells, Vehicle, 24 h, MS-137

description: Control


title: S_0min_C

value: Wild-type


title: ctrl_AAV_WT_rep1


title: P1_25h_B


title: P5_25h_B


title: ctrl_AAV_R6/1_rep2


title: Renal tube epithelial cells, Vehicle, 9 h, MS-123

description: Control

value: Sprague-Dawley Rat


title: P3_25h_B


title: Renal tube epithelial cells, Vehicle, 9 h, MS-125

description: Control

value: Kidney


title: R6/1_rep1 [8 weeks]

description: processed data file: RNAseq__R6-1_8wks__processed_All_exp_f0.1_test_20140301.txt

value: 8 weeks


title: Renal tube epithelial cells, Vehicle, 9 h, MS-124

description: Control

value: Renal tube epithelial cells


title: R6/1_rep2 [8 weeks]


title: S_25h_B


title: WT_rep3 [R6/1 8 weeks]


title: S_15min_C


title: S_9h_B


title: P1_15min_C


title: OT1_0_1percent

city: Cambridge

first: Ang

middle: Andy

last: Tu

state: MA

address: 500 Main Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

description: WT B6 spiked with 0.1 percent OT-1 Rag+/+

data_processing:
Illumina bcl2fastq2.17.1.14 was used to generate fastqs from bcl files
STAR was used to align the scRNA-seq data
Regression analysis was done as described in manuscript
Genome_build: mm10

source_name: Transcriptome of single cells

extract_protocol:
Seq-Well
Illumina Nextera XT

tag: stimulation

tag: sample type

value: Magnetic-beads enriched T cells


title: WT_rep2 [R6/1 8 weeks]


title: Renal tube epithelial cells, Vehicle, 9 h, MS-122

description: Control

value: 9 h


title: Donor_1 cALL_RNS_01

description:
Donor_1
Gene expression data of peripheral blood mononuclear cells


title: OT1_0_01percent

description: WT B6 spiked with 0.01 percent OT-1 Rag+/+


title: Donor_2 cALL_RNS_02

description:
Donor_2
Gene expression data of peripheral blood mononuclear cells

value: B-other


title: Renal tube epithelial cells, Vehicle, 9 h, MS-121

description: Control

value: Control

value: Vehicle


title: S_3h_B


title: OT1_1percent

description: WT B6 spiked with 1 percent OT-1 Rag+/+


title: WT_rep1 [R6/1 8 weeks]


title: Renal tube epithelial cells, Vehicle, 24 h, MS-136

description: Control


title: Primary hepatocytes, High, 24 h, MS-120

description: Treatment

source_name: Primary hepatocytes, High (0.125 mM)

value: Liver

value: Primary hepatocytes

value: thioacetamide-S-oxide


title: OT1_10percent

description: WT B6 spiked with 10 percent OT-1 Rag+/+


title: R6/1_rep3 [8 weeks]


title: S_1h_B


title: Primary hepatocytes, High, 24 h, MS-119

description: Treatment


title: Mouse4_exvivo

value: Tetramer-sorted CD8


title: R6/1_rep2 [4 weeks]

description: processed data file: RNAseq__R6-1_4wks__processed_All_exp_f0.1_4wk_20140301.txt

value: 4 weeks

value: Striatum


title: R6/1_rep3 [4 weeks]


title: P5_15min_B

value: Bioreactor with low glucose content


title: Primary hepatocytes, High, 24 h, MS-118

description: Treatment


title: P3_15min_B

value: Wild-type


title: P1_15min_B


title: Mouse3_exvivo


title: WT_rep3 [R6/1 4 weeks]


title: Primary hepatocytes, High, 24 h, MS-116

description: Treatment

value: Sprague-Dawley Rat


title: Mouse1_exvivo


title: Mouse2_exvivo


title: S_15min_B


title: WT_rep2 [R6/1 4 weeks]


title: S_0min_B


title: Mouse4_Stimulated

value: Antigen


title: Primary hepatocytes, High, 9 h, MS-105

description: Treatment


title: WT_rep1 [R6/1 4 weeks]


title: P5_25h_A


title: Mouse3_Stimulated


title: Primary hepatocytes, High, 9 h, MS-104

description: Treatment


title: Primary hepatocytes, High, 9 h, MS-103

description: Treatment


title: Mouse2_Stimulated


title: P3_25h_A


title: CHL2_rep3

description: processed data file: RNAseq__CHL2_1yr__processed_exp_f0.1_test_20140301.txt

value: 1 year


title: CHL2_rep2


title: R6/1_rep1 [4 weeks]


title: Primary hepatocytes, High, 9 h, MS-102

description: Treatment


title: Primary hepatocytes, High, 24 h, MS-117

description: Treatment


title: CHL2_rep1


title: WT_rep2 [CHL2]


title: S_9h_A


title: S_25h_A


title: Primary hepatocytes, High, 9 h, MS-101

description: Treatment


title: Mouse1_Stimulated


title: Primary hepatocytes, Low, 24 h, MS-114

description: Treatment

source_name: Primary hepatocytes, Low (0.025 mM)


title: WT_rep3 [CHL2]


title: P1_25h_A


title: S_3h_A


title: WT_rep1 [CHL2]


title: S_1h_A


title: Donor_9 cALL_RNS_09

description:
Donor_9
Gene expression data of peripheral blood mononuclear cells

value: female

value: positive

value: non-B-other


title: Hcau_FH

city: Temuco

first: Giovanni

middle: A

last: Larama

address: Francisco Salazar 01145

department: Ingenieria Matematica

country: Chile

institute: Universidad de La Frontera

data_processing:
Reads were trimmed using NGSQCToolkit v2.3
Relative abundance was calculed using RSEM v1.2.26 which uses bowtie v1.1.1
Genome_build: Hcaudiculatum_2019.fasta
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample

organism: Hymenophyllum caudiculatum

source_name: whole plant

extract_protocol:
Plant tissue was pulverized with liquid nitrogen and total RNA extracted using UltraClean Plant RNA isolation kit (Mo Bio)
as described by Macrogen Inc for total RNA samples

value: whole plant

tag: treatment

value: Hydrated state


title: Hcau_RH

value: Rehydrated state


title: Primary hepatocytes, Low, 24 h, MS-113

description: Treatment

tag: strain

value: Liver


title: Hcau_DH

value: Dehydrated state


title: P5_15min_A


title: BAG neurons, AX7210-6

first: Isabel

last: Beets

address: Francis Crick Avenue

department: Cell Biology

institute: MRC-LMB

description:
samples.csv_DESeq_results_4_peat.txt
samples.csv_DESeq_norm_read_counts.txt
samples.csv_tpm.txt

data_processing:
ribosomal RNA removal using bowtie2 version 1.1.2 flags used: --phred33; -D 20; -R 3; -N 1; -L 20; -i S,1,0.50; -X 1000; –dovetail; --np 0
merged files - samples were sequenced over multiple lanes. This was done using commands zcat & pigz
Data processed using PRAGUI pipeline utilising the RNA-Seq packages detailed in further steps below
quality and adapter trimming of FastQ files using Trim Galore!
aligning of reads using STAR with the following flags --outSAMstrandField intronMotif; --readFilesCommand zcat -c; --outSAMtype BAM SortedByCoordinate
Differential analysis using DESeq2
Genome_build: C. elegans PRJNA13758 WS255 genomic
Supplementary_files_format_and_content: Tab-delimited text files including transcripts per million values and normalized read counts:
samples.csv_DESeq_results_4_peat.txt (Input file for PEAT exploratory analysis software)
samples.csv_DESeq_norm_read_counts.txt (DESeq2 normalized read counts)
samples.csv_tpm.txt (TPM values)

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: FAC-sorted BAG neurons

growth_protocol: C. elegans were cultivated on standard nematode growth medium (NGM) seeded with a bacterial lawn of Escherichia coli OP50, and kept at 20 degrees celcius.

extract_protocol:
BAG neurons were specifically labeled by expressing a flp-17p::gfp transgene, and isolated from acutely dissociated adult animals using FACS. An average of 4000 cells per sample was directly sorted in cell lysis buffer (0.2% Triton X-100 and 2 U/μl Rnase inhibitor), and processed using a Smart-seq2 protocol (Picelli et al., Nature Protocols, Vol 9 (1), pp 171-181, 2014)
Libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: day 1 adult

value: FAC-sorted BAG neurons


title: Primary hepatocytes, Low, 24 h, MS-115

description: Treatment

value: Primary hepatocytes

tag: agent

value: thioacetamide-S-oxide


title: Verde_Trat48hr_2

city: Cuernavaca

first: Veronica

last: Jimenez-Jacinto

state: Morelos

address: Av. Universidad 2001. Col. chamilpa

department: Unidad Universitaria de Secuenciación Masiva y Bioinformática

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

description:
Vanilla planifolia Jacks.
processed data: Verde_Trat48hrvsAmarillo_Ctr10hr_Intersect.txt

data_processing:
Bc2fastq 2.17: To make call bases
FastQC: To check Quality Reports
smalt: To Alingner vs Pathogen to filtering
Trinity: To build Transcript assembly
RSEM: To build Counts table and generation of normalized abundance measurements
BUSCO: Provides quantitative measures for the assessment of genome assembly
Blast2GO: To make Annotation
IDEAmex: To analyze Differential Expression
Genome_build: Trinity.fasta
Supplementary_files_format_and_content: *_Intersect.txt: Tab-delimited text files with the following columns: logarithm base 2 of fold Change (logFC), logCoutPerMillon (logCPM), Pvalue, False Discovery Rate (FDR), columns for each sample with raw counts, and columns with normalized counts for each sample, results of Differential Expression, and Regulation.

organism: Vanilla planifolia

source_name: Root

growth_protocol: Briefly, cuttings of V. planifolia Jacks were subjected to darkness during ten days. The absence of light exposition allowed the generation of new roots.

extract_protocol:
For the total RNA extraction from the roots of Vanilla planifolia Jacks, a protocol was standardized based on what was described by Valderrama-Chairez et al., 2002; which included the extraction of total RNA from 200 mg of root tissue with the help of Trizol Reagent, a treatment with Phenol: chloroform: Isoamyl Alcohol 25: 24: 1, and the subsequent cleaning of the RNA obtained, using silica columns included in the SV Total RNA Isolation System extraction kit from Promega.
TruSeq stranded mRNA sample preparation kit.

treatment_protocol: Fusarium infection in vanilla roots.

value: Root

value: Fusarium oxysporum f. sp. vanillae infection

tag: timepoint

value: 2 days


title: Verde_Trat48hr_3


title: BAG neurons, AX7210-5


title: P3_15min_A

value: Bioreactor with low glucose content

value: Wild-type


title: Verde_Trat48hr_1


title: Primary hepatocytes, Low, 24 h, MS-111

description: Treatment

value: Sprague-Dawley Rat


title: Primary hepatocytes, Low, 9 h, MS-99

description: Treatment

value: 9 h


title: Primary hepatocytes, Low, 24 h, MS-112

description: Treatment


title: Rojo_Trat10d_5

description:
Vanilla planifolia Jacks.
processed data: Rojo_Trat10dvsAzul_Ctr48hr_Intersect.txt

value: 10 days


title: Primary hepatocytes, Low, 9 h, MS-98

description: Treatment


title: BAG neurons, AX7210-3


title: Primary hepatocytes, Low, 9 h, MS-97

description: Treatment


title: BAG neurons, AX7210-2


title: S_15min_A


title: Primary hepatocytes, Low, 9 h, MS-96

description: Treatment


title: BAG neurons, AX7210-4


title: S_0min_A


title: Rojo_Trat10d_1


title: Primary hepatocytes, Low, 9 h, MS-100

description: Treatment


title: BAG neurons, AX7210-1


title: P1_15min_A


title: Azul_Ctr48hr_1

value: Control


title: Azul_Ctr48hr_3


title: Isoleucine Starvation + Rifampicin 45min

city: København N

first: Bertil

last: Gummesson

address: OLE MAALØES VEJ 5

department: Department of Biology

country: Denmark

institute: University of Copenhagen

description: Escherichia coli K-12 + 1% Escherichia coli B

data_processing:
The reads were aligned to Escherichia coli str. K-12 substr. MG1655 (RefSeq NC_U00096.3) using bwa-aln (version 0.7.15.2 with default parameters). The tool was used  at the public server usegalaxy.org
Reads were counted using htseq-count (version 0.6.1p1)
In parallel and similarly, the reads were aligned (bwa-aln) to the reference sequence of the plasmid harboring the spike-in genes and the features (qrr2, bla, and lacI) from the plasmid counted using htseq-count.
Read counts were normalized to gene size prior normalization to spike-in reads to give RPKSP (Gene read counts).  Reads Per Kilobase of gene per 10 kilobase of Spike-in and as a comparison (Spike-in plasmid gene read counts).  The read counts were also normalized according to standard method to give RPKM, Reads Per Kilobase Million (Normalized gene expression data).
Genome_build: RefSeq NC_U00096.3, pQrr2
Supplementary_files_format_and_content: Tab-delimited text files including RPKSP and RPKM values for all genes in each Sample.

organism:
Escherichia coli B
Escherichia coli K-12

source_name: 1% spike-in + Whole cell culture

growth_protocol: Cells were grown at 37°C at 200 rpm in morpholinepropanesulfonic acid (MOPS) minimal medium supplemented with 0.2% glucose. Cell growth was monitored spectrophotometrically by optical density at 423 nm and cultures were grown for at least 9 generations in exponential phase before sampling.

extract_protocol:
RNA was isolated by using a hot acidic phenol extraction method
RNA libraries were prepared for sequencing by GATC BIOTECH using standard Illumina protocols without prior rRNA depleation

treatment_protocol: Isoleucine starvation was induced by adding valine to a final concentration of 400 µg/ml. Rifampicin was added to a final concentration of 300 µg/ml. Prior to total RNA extraction, 1% spike-in culture were added to each sample based on sample OD

tag: strains

value: rph+ gatC+ glpR+

value: cells 45  minute after rifampicin addition


title: Primary hepatocytes, Vehicle, 9 h, MS-95

description: Control

source_name: Primary hepatocytes, Vehicle

value: Liver

tag: cell type

value: Vehicle


title: Azul_Ctr48hr_2


title: BAG neurons, AX7207-4

value: day 1 adult


title: BAG neurons, AX7207-5

value: FAC-sorted BAG neurons


title: Isoleucine Starvation + Rifampicin 15min

value: cells 15  minute after rifampicin addition


title: Primary hepatocytes, Vehicle, 9 h, MS-94

description: Control

value: Primary hepatocytes

tag: dose


title: BAG neurons, AX7207-6


title: BAG neurons, AX7207-3


title: Amarillo_Ctr10hr_3

tag: tissue

value: Root

value: 10 hr


title: Isoleucine Starvation + Rifampicin 10min

value: cells 10  minute after rifampicin addition


title: Isoleucine Starvation 80min

value: 80 minute Isoleucine starved cells


title: Primary hepatocytes, Vehicle, 9 h, MS-93

description: Control

tag: duration


title: Primary hepatocytes, Vehicle, 9 h, MS-92

description: Control


title: BAG neurons, AX7207-2


title: Amarillo_Ctr10hr_1


title: Isoleucine Starvation + Rifampicin 25min

value: cells 25  minute after rifampicin addition


title: Isoleucine Starvation 40min

value: 40 minute Isoleucine starved cells


title: Primary hepatocytes, Vehicle, 9 h, MS-91

description: Control

value: Sprague-Dawley Rat

value: 9 h


title: INT-3

city: Lausanne

first: Gaby

last: El Alam

state: Vaud

address: Station 15

department: SV LISP

country: Switzerland

institute: École polytechnique fédérale de Lausanne

description: GFP+ cells sorted by FACS pooled from 4 mice on day 3 and treated with INT-777

data_processing:
FastQC (default parameters) was used to verify the quality of the mapping. No low-quality reads were present and no trimming was needed.
generate STAR (version 2.73a) genome indexes with following parameters: STAR --runThreadN 16 --runMode genomeGenerate --limitGenomeGenerateRAM 33524399488 --genomeFastaFiles Mus_musculus.GRCm38.dna_rm.primary_assembly.fa --sjdbGTFfile GRCm38/release95/Mus_musculus.GRCm38.95.gtf --sjdbOverhang 99
Map paired reads for each sample using STAR (version 2.73a) aligner with the following parameters: STAR --runThreadN 16 --genomeDir ./Data/stargenome/$STARGENOMENAME --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --quantMode GeneCounts --readFilesIn $R1 $R2 --outFileNamePrefix ./Data/mapped/$SAMPLE
Counts for each sample features (outputed by STAR) where read into R
The obtained STAR gene-counts for each alignment were analyzed for differentially expressed genes using the R package edgeR (version 3.24.3) using a generalized-linear model. The trimmed mean of M values (TMM) method was chosen to normalize the counts and the Cox-Reid common dispersion method for computing the dispersion parameter (tag wise dispersion was also computed).
A principal component analysis of the data reveals the presence of a batch effect with the third batch (day 3)
The RUVSeq (version 1.16.1) Bioconductor R package was used to correct for the unwanted variation caused by the batch effect. Empirical control genes were identified based on first-pass differential expression analysis were used for RUVg normalization.
A threshold of 1 log2 fold change and p-value larger than 0.05 were considered when identifying the differentially expressed genes.
The clusterProfiler (version 3.10.1) package was then used to explore GO enrichment of the obtained results.
enriched transcription factor binding motifs were identified using the up-regulated gene list previously obtained using the RcisTarget (version 1.2.1) R package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw mapped read counts per feature (generated by STAR - per strand and combined strands)

source_name: intestine

growth_protocol: ISC culture medium was the crypt culture medium containing JAG-1 (1µM; Anaspec) and CHIR99021 (3 μM; Millipore).

extract_protocol:
RNAqueous kit (invitrogen)
BGISEQ-500 PE100

treatment_protocol: Cells were treated with INT-777 30uM

value: intestinal stem cells

tag: strain/genotype

value: intestine

tag: concentration

tag: total mass

tag: rin


title: Isoleucine Starvation 10min

tag: genotype

value: rph+ gatC+ glpR+

value: 10 minute Isoleucine starved cells


title: Primary hepatocytes, Vehicle, 24 h, MS-184

description: Control

value: Liver

value: Control

value: Vehicle


title: Isoleucine Starvation 5min

value: 5 minute Isoleucine starved cells


title: Isoleucine Starvation 20min

value: 20 minute Isoleucine starved cells


title: Primary hepatocytes, Vehicle, 24 h, MS-185

description: Control

value: Primary hepatocytes


title: Hdent_RH

data_processing:
Reads were trimmed using NGSQCToolkit v2.3
Relative abundance was calculed using RSEM v1.2.26 which uses bowtie v1.1.1
Genome_build: Hdentatum_2019.fasta
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample

organism: Hymenophyllum dentatum

value: whole plant

value: Rehydrated state


title: Hdent_DH

value: Dehydrated state


title: INT-1

description: GFP+ cells sorted by FACS pooled from 4 mice on day 1 and treated with INT-777


title: Primary hepatocytes, Vehicle, 24 h, MS-183

description: Control


title: Steady State replicate 3

value: Steady state


title: S. sonnei infected larvae 3

organism:
Shigella sonnei
Danio rerio

source_name: pool of 20 S. sonnei infected zebrafish larvae

growth_protocol: Larvae were obtained by natural spawning and maintained at 28.5C until 3 days post fertilisation in 0.5xE2 medium (7.5 mM NaCl, 0.25 mM KCl, 0.5 mM MgSO4, 75 µM KH2PO4,  25 µM Na2HPO4, 0.5 mM CaCl2, 0.35 mM NaHCO3). For injections, larvae were then anaestesised in 0.5xE2 medium supplemented with 200 ug/ml tricaine, and injected with bacterial resuspension buffer alone (2% polyvinylpyrrolidone, 0.5% phenol red in phosphate buffer saline). Injected larvae were then returned in E2 medium without anesthetic and maintained at 28.5C for 24h before collection. Bacteria for injections were firsts grown at 37C O/N from glycerol stocks on tryptic soy agar plates containing 0.01% Congo red and 100 ug/ml Carbenicillin. One single smooth colony accumulating Congo red was selected and cultured O/N in tryptic soy broth containing 100 ug/ml Carbenicillin  at 37C with agitation. O/N culture was then diluted 50x in tryptic soy broth containing 25 ug/ml Carbenicillin and grown at 37C with agitation until culture reached an OD of 0.55-0.65 at 600 nm. Bacteria were then spun down, washed in PBS and resuspended at 7000 CFU/nl in bcterial resuspension buffer for injections.

value: AB (zebrafish), 53G transformed with pFPV25.1 (S. sonnei)

tag: infection

value: Shigella sonnei

tag: incubation temperature

tag: collection point

value: 24 hours post injection


title: S. sonnei infected larvae 2

description: ssonnei_processed_data.tsv, zebrafish_processed_data.tsv

tag: strain


title: S. sonnei infected larvae 1


title: Amarillo_Ctr10hr_2

value: Root

tag: treatment

value: 10 hr


title: Steady State replicate 2

value: rph+ gatC+ glpR+


title: Primary hepatocytes, Vehicle, 24 h, MS-181

description: Control

value: Sprague-Dawley Rat

tag: agent


title: Primary hepatocytes, Vehicle, 24 h, MS-182

description: Control

value: Liver


title: Steady State replicate 1


title: DMSO-2

description: GFP+ cells sorted by FACS pooled from 4 mice on day 2 and treated with DMSO

value: intestinal stem cells

value: intestine

value: DMSO 12h


title: Intermediate-activity sgRNA perturb-seq experiment sgRNA barcode reads (gemgroup2)

status: Public on Nov 18 2019

city: Boston

first: Marco

last: Jost

address: 77 Ave Louis Pasteur, NRB848

institute: Harvard Medical School

description: sgRNA barcode reads, gemgroup 2

data_processing:
Fastq.gz files were generated from raw Illumina BCL files using bcl2fastq
BAM files were generated from the fastq.gz files using 10X Genomics Cellranger version 2.1.1 with default paramaters (cellranger count).
Read 1: 26, Index read 1 (i7): 8, Read 2: 98
Custom paired end, all 3 reads informative
Reads from multiple channels (gemgroups) of the 10X run were combined using 10X Genomics Cellranger version 2.1.1 (cellranger aggr)
Gene-barcode matrices were determined using 10X Genomics Cellranger version 2.1.1 with default parameters
Guide barcode identities were determined as described in the paper.
Genome_build: hg38
Supplementary_files_format_and_content: BAM files were generated by cellranger and contain raw reads for single-cell RNAseq, including cell identity, UMI information, and gemgroup id (referred to in guide barcode filenames). Gene-barcode matrices are the UMI-collapsed counts of these reads, representing counts of molecules per cell as determined and filtered by cellranger. These are provided in the format outputted by cellranger: the matrix itself is in matrix market exchange format, with the rows (cell barcodes) and columns (gene identities) labels given in TSV format as described in the cellranger documentation. Guide barcodes were specifically amplified from the RNA-seq libraries and sequenced to higher coverage, and then identities were called as discussed in the paper.

source_name: K562 cells

growth_protocol: K562 cells expressing dCas9-KRAB were transduced with lentivirus carrying the sgRNA expression cassettes and a BFP marker. Transduced cells were isolated by FACS 3 days after transduction and grown for 2 additional days. Growth was performed in RPMI media supplemented with FBS and Pen/Strep/Gln.

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium instrument
Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide (v2 chemistry)

tag: cell line

value: K562 chronic myelogenous leukemia cell line


title: Intermediate-activity sgRNA perturb-seq experiment sgRNA barcode reads (gemgroup3)

description: sgRNA barcode reads, gemgroup 3


title: Intermediate-activity sgRNA perturb-seq experiment (gemgroup2)

description:
Single-cell RNA-seq data, gemgroup 2
10X_barcodes.tsv
10X_genes.tsv
10X_matrix.mtx
cell_identities.csv


title: Intermediate-activity sgRNA perturb-seq experiment (gemgroup3)

description:
Single-cell RNA-seq data, gemgroup 3
10X_barcodes.tsv
10X_genes.tsv
10X_matrix.mtx
cell_identities.csv


title: Intermediate-activity sgRNA perturb-seq experiment sgRNA barcode reads (gemgroup1)

description: sgRNA barcode reads, gemgroup 1


title: GM day 6

city: Leuven

first: Tim

last: Herpelinck

address: Herestraat 49

department: Development and Regeneration

country: Belgium

institute: KU Leuven

data_processing:
Demultiplexing  of the Illumina sequencer's base call files into fastq files was performed with Cell Ranger (v. 2.1.1) mkfastq pipeline.
Sequenced reads were processed with the Cell Ranger count pipeline to assign barcodes and count UMIs. The final raw dataset was built using the Cell Ranger aggregation pipeline without applying any normalisation method.
The scater R-package (v. 1.12.2) was used for quality control and filtering. Genes not expressed in any cell were removed. Cells with quality control metrics deviating more than 3 absolute standard deviations from the median were classified as outliers. Genes with an average count below a filter threshold of 0.001 were filtered out. Genes with duplicated names were removed.
The filtered matrix was loaded into the Seurat package (v. 2.3.4) and log-normalised with a scale factor of 10000. The FindVariableGenes function was used to find highly variable genes, which were used for downstream analysis. The data was centred and scaled using a linear regression model, regressing out the percentage of mitochondrial genes per cell.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files of normalised counts for each sample.

source_name: Periosteum

growth_protocol: All cells were expanded up to passage 5 in high-glucose DMEM-GlutaMAX supplemented with 10% foetal bovine serum, 1% sodium pyruvate and 1% antibiotics-antimycotic solution, further referred to as growth medium (GM).

extract_protocol:
Cells were released enzymatically from the culture flasks by incubation with TrypLE Express (Gibco, cat #12605-036) for 10 minutes, spun down at 200g for 10 minutes and resuspended at a cell density of 1 million cells/ml in 0.1% BSA-PBS.
Libraries were prepared using the Chromium Single Cell 3’ Reagent Kit (v2 Chemistry, 10x Genomics) according to the manufacturer’s instructions. Briefly, Gel bead-in-Emulsions (GEMs) were generated using the Chromium Single Cell Controller. Following reverse transcription, the single-cell droplets were broken. Single-strand cDNA was purified with Cleanup Mix containing Silane DynaBeads (Thermo Fisher Scientific) and subsequently amplified. Next, the SPRIselect Reagent Kit (Beckman Coulter) was used for fragmentation, end-repair, A-tailing and index adaptor ligation. Final libraries were obtained after amplification and subsequent clean-up of the ligated strands with SPRIselect beads. Sequencing of the libraries was performed on the HiSeq4000 System (Illumina) using the following parameters: 26 bp read 1 – 8 bp index 1 – 98 bp read 2

treatment_protocol: For preconditioning, cells were cultured for six days in serum free chemically-defined medium with the removal of the growth factor cocktail, beta-glycerophosphate and lineolic acid (patent US20010039050)(Harrison, 1991).

value: Periosteum

tag: passage


title: INT-2

description: GFP+ cells sorted by FACS pooled from 4 mice on day 2 and treated with INT-777

tag: cell type


title: BAG neurons, AX7207-1

tag: developmental stage

value: day 1 adult

value: FAC-sorted BAG neurons


title: Intermediate-activity sgRNA perturb-seq experiment (gemgroup1)

description:
Single-cell RNA-seq data, gemgroup 1
10X_barcodes.tsv
10X_genes.tsv
10X_matrix.mtx
cell_identities.csv


title: AS1960

city: PARIS

first: Pauline

last: ARNAUD

address: 46, rue Henri Huchard

country: France

institute: AP-HP - Hôpital Bichat

data_processing:
Random read removal from all samples to correct for read imbalances (after the read removal all samples have the read count of that sample with the lowest read count); custom C# script
Alignement to Reference genome; Tophat 2.0.8, samtools-0.1.7, bowtie 2.1.0
Identification of average gene expression values in SMCs from MFS patients and control subjects and differentially expressed genes; Cufflinks 1.3.0
Genome_build: hg19
Supplementary_files_format_and_content: cuffdiff output including average gene expression values in SMCs from MFS patients and control subjects and differential expression values
Supplementary_files_format_and_content: List of differentially expressed genes in SMCs derived from MFS patients and control subjects

source_name: outer curvature of Thoracic Ascending Aorta

growth_protocol: Aortic tissues were processed to separate medial and adventitial layers. Media samples were incubated in collagenase and elastase 0.1% (3 h, 37°C) to obtain SMCs that were cultured in specific medium (Promocell) containing 20% fetal calf serum (FCS), insulin (5 μg/mL), human epidermal and fibroblast growth factors (0.5 and 2 ng/mL, respectively), plasmocin (2.5 μg/ml) and primocin (100 μg/ml).

extract_protocol:
Cells at passages 3–4 were used for RNA extraction performed after 24 hr incubation in serum free medium. Total RNA was extracted from human SMC cultures with Trizol® Reagent (Life Technologies), purified by miRNeasy Mini kit® (Qiagen S.A.) according to the manufacturer’s instructions. DNase digestion procedure was followed for each sample.
Libraries were prepared from 1μg of total RNA using TruSeq Stranded mRNA kit protocol (Illumina®) according to the supplier’s recommendations. Briefly, poly-A RNA was isolated using oligo-dT25 attached to magnetic beads, fragmented into ~300 SCP-long pieces using divalent cations under elevated temperature, used as template for double-stranded cDNA synthesis, Illumina adapters ligation and PCR-mediated cDNA library amplification. Sequencing was carried out on Illumina HiSeq4000,

tag: tissue

value: primary smooth muscle cells

tag: passages

tag: disease state

value: control


title: FB490

value: outer curvature of Thoracic Ascending Aorta

value: Marfan Syndrome patient


title: FB721


title: AS1883


title: Hdent_FH

value: whole plant

value: Hydrated state


title: DMSO-3

description: GFP+ cells sorted by FACS pooled from 4 mice on day 3 and treated with DMSO

tag: strain/genotype

tag: concentration


title: FB359


title: AS1043


title: Low Cell CTCF siRNA 144hrs CTCF Rep2

city: Darlinghurst

first: Amanda

last: Khoury

state: NSW

address: 384 Victoria St.

country: Australia

institute: Garvan Institute

data_processing:
Fastq file analysis was performed using a custom pipeline based on a modified version of Guidelines for Molecular Identifier (MID) Analysis for Single-Read Sequencing (Active Motif)
Fastq files were merged by a custom script, adapter trimmed using cutadapt and read quality was assessed using FastQC.
Reads were aligned to the human (hg19) genome using BWA and the resulting SAM file was sorted and converted into BAM format
Duplicate reads were identified and removed using custom Perl script provided by Active Motif
The de-duplicated BAM was used to generate bigwig files and peak call with MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak

source_name: IMR90 lung fibroblasts

growth_protocol: IMR90 cells were cultured under ATCC recommended conditions at 37°C and 5% CO2.

extract_protocol:
Cells were harvested according to Active Motif Low-Cell ChIP-seq kit (Cat no. 53084)
Libraries were prepared according to Active Motif Low-Cell ChIP-seq kit (Cat no. 53084)
Low Cell ChIP-seq

treatment_protocol: IMR90 cells were transfected with 20nM of Dharmacon ON-TARGET plus pooled Non-targeting siRNA or 20nM of Dhamacon ON-TARGET plus pooled CTCF siRNA (containing sequences GAUGAAGACUGAAGUAAUG, GGAGAAAGAAGAAGAGUA, GAAGAUGCCUGCCACUUAC, GAACAGCCCAUAAACAUAG) according to the manufacturer-supplied protocol. Following 72hrs of transfection, cells were split and reverse transfected for a further 72hrs (144hrs).

value: IMR90 lung fibroblasts

tag: chip antibody

value: CTCF

value: 20nM CTCF siRNA pool

tag: time


title: DMSO-1

description: GFP+ cells sorted by FACS pooled from 4 mice on day 1 and treated with DMSO

tag: total mass

tag: rin


title: Low Cell CTCF siRNA 144hrs CTCF Rep1


title: CDM day 6


title: Low Cell Control siRNA 144hrs CTCF Rep2

value: 20nM Non-Target siRNA pool


title: Low Cell Control siRNA 144hrs CTCF Rep1


title: SC-WT-monocytes

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Transcript abundance estimated by Salmon 0.14.1 (PMID: 28263959) based on whole transcripts annotation by gencode vM22 (PMID: 22955987).
Genome_build: mm10
Supplementary_files_format_and_content: Txt file, output from salmon columns from left to right represent "Name", "Length", "EffectiveLength", "TPM" (transcripts per million pair-end reads), and "NumReads".

source_name: monocytes isolated from the spinal cord following EAE induction

extract_protocol:
RNA from the purified monocytes and monocyte-derived cells was isolated using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany).
RNA-Seq libraries were built using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Wilmington MA, USA) with 300 ng of total RNA and 11 cycles of PCR according to manufacturer’s recommendation. The libraries were quantified using Qubit Fluorometer, and the quality of the libraries was determined by Bioanalyzer High Sensitivity DNA Analysis (Agilent, Santa Clara, CA, USA).

treatment_protocol: Experimental autoimmune encephalomyelitis (EAE) was induced in mice on a C57BL/6J background by subcutaneously injection of myelin oligodendrocyte glycoprotein peptide emulsified in complete Freund’s adjuvant. Pertussis toxin (250 ng) was injected intraperitoneally at 2- and 24-hours following the injection of emulsion.

value: Spine cord

value: Monocytes


title: SC-WT-APC

source_name: monocyte-derived antigen-presenting cells isolated from the bone marrow following EAE induction

value: Antigen presenting cells


title: IMR90_CTCF siRNA 144hrs CTCF Rep2

data_processing:
Bowtie1 (Langmead et al., 2009) was used to align ChIP-seq reads to hg19 allowing up to three mismatches, discarding reads mapping to multiple positions in the genome and removing duplicate reads.
Peaks were called using MACS2 (Zhang et al., 2008) or Peak ranger software (Feng et al., 2011)
Genome_build: hg19
Supplementary_files_format_and_content: bed, narrowPeak

growth_protocol: LNCaP were cultured under ATCC recommended conditions at 37°C and 5% CO2.

extract_protocol:
Cells were scraped into ice-cold PBS containing protease inhibitors and collected by centrifugation at 500g for 5 minutes at 4˚C. Pellet was resuspended in ice-cold PBS and fixed with 1% formaldehyde for 15 minutes at room temperature. Fixation was quenched with addition of 125mM (final concentration) glycine for 5 minutes at room temperature. Fixed cells were centrifuged at 500g for 5 minutes at 4˚C and washed 2x with 10mls ice-cold PBS containing protease inhibitors. Pellet was resuspended in 1.5ml nuclei extraction buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1mM EDTA and 0.5% IGEPAL) per 10x106 cells and incubated on ice for 10 minutes. Suspension was dounced 10x with a tight dounce and centrifuged at 1000g for 5 minutes at 4˚C. Pellet was washed 1x with ice-cold PBS containing protease inhibitors and centrifuged. Pellet was resuspended in 1x sonication buffer (50mM Tris-HCl pH 8, 1% SDS, 10mM EDTA) and fragmented to ~300bp using a Branson probe Sonifier. Fragmented DNA was centrifuged and verified to be the correct size using gel electrophoresis. Pelleted DNA was resuspended in 1ml IP dilution buffer (16.7mM Tris-HCl pH 8, 0.01% SDS, 1% Triton X-100, 167mM NaCl, 1.2mM EDTA) per ChIP (each ChIP contains 5x106 cells) cells and pre-cleared with 30ul of Salmon Sperm DNA/Protein A agarose-50% Slurry (Millipore #16-157) per ChIP. 10ug of the following antibodies were added per ChIP and incubated overnight– CTCF (#07-729, Millipore), H3K4me3 (#39159, Active Motif), H3K27ac (#39133, Active Motif). Antibody/protein complexes were bound to Salmon Sperm DNA/Protein A agarose-50% Slurry. The samples were pelleted and washed once with low salt buffer (2mM EDTA, 0.1% SDS, 1% Triton X-100, 20mM Tris-HCl pH8.1, 150mM NaCl) once with high salt buffer 2mM EDTA, 0.1% SDS, 1% Triton X-100, 20mM Tris-HCl pH8.1, 500mM NaCl), once with LiCl buffer (1mM EDTA, 10mM Tris-HCl pH8.1, 250mM LiCl, 1% sodium deoxycholate, 1% IGEPAL) and twice with TE buffer (1mM EDTA, 10mM Tris HCl pH 8.1). Antibody/protein complexes were eluted off beads using elution buffer (1% SDS, 100mM sodium bicarbonate). Crosslinks were reversed with NaCl. Protein and RNA were degraded with Proteinase K and RNAse A, respectively.
Libraries were prepared using TruSeq ChIP sample Preparation Kit (Catalog # IP-202-900).

treatment_protocol: LNCaP cells were transfected with 20nM of Dhamacon ON-TARGET plus pooled Non-targeting siRNA or 20nM of Dhamacon ON-TARGET plus pooled CTCF siRNA (containing sequences GAUGAAGACUGAAGUAAUG, GGAGAAAGAAGAAGAGUA, GAAGAUGCCUGCCACUUAC, GAACAGCCCAUAAACAUAG) according to the manufacturer-supplied protocol. Following 72hrs of transfection, cells were split and reverse transfected for a further 72hrs (144hrs).


title: BM-WT-monocytes

source_name: monocytes isolated from the bone marrow following EAE induction

value: Bone marrow


title: IMR90_Control siRNA 144hrs CTCF Rep1


title: IMR90_Control siRNA 144hrs CTCF Rep2


title: Pat9_WM_2_6

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

institute: University Medical Center Freiburg

description: library of 192 cells

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: Human brain surgery sample

extract_protocol:
Fresh tissue was dissected by removing the meninges. Single-cell suspesions were generated with a dounce potter followed by passing through a cell strainer. Myelin was removed using percoll gradient centrifugation.
As described in mCEL-Seq2 protocol (Hashimshony et al. 2016 and Herman et al. 2018)
Adapted from TruSeq Small RNA Library Preparation Protocol

value: Brain

tag: diagnosis

value: Control

tag: region

value: Temporal lobe


title: Pat9_WM_1_5

description: library of 192 cells


title: Pat9_GM_2_2

description: library of 192 cells


title: LNCaP_CTCF siRNA 144hrs CTCF Rep2

source_name: LNCaP Prostate Cancer Cells

value: LNCaP Prostate Cancer Cells

tag: treatment


title: LNCaP_CTCF siRNA 144hrs CTCF Rep1


title: Pat9_GM_1_1

description: library of 192 cells


title: Rojo_Trat10d_2

value: Root

value: Fusarium oxysporum f. sp. vanillae infection

tag: timepoint

value: 10 days


title: IMR90_CTCF siRNA 144hrs CTCF Rep1

tag: cell line


title: 48-72h_5

city: Edinburgh

first: Amy

last: Buck

address: Ashworth Labs, Charlotte Auerbach Road

department: IIIR

institute: The University of Edinburgh

data_processing:
Primers were trimmed from the raw fastq format sequence data using cutadapt software (v1.9.1; parameters -O 6 -m 16 -n 5 -q 20).
Only trimmed reads that contained the adapter, were 16nt or greater in length and were present at 2 or more copies per sample were retained.
Simple scripts were used to generate non-redundant sequence sets (collapsed) in fasta format from each sample.
Genome_build: https://parasite.wormbase.org/Litomosoides_sigmodontis_prjeb3075 version nLs.2.1
Supplementary_files_format_and_content: Processed data files contain the non-redundant trimmed sequences from each sample (sequence and counts).

organism: Litomosoides sigmodontis

source_name: adult female worms ES products 72h

growth_protocol: Parasites were obtained at different time points post-infection from Meriones unguiculatus, and cultured in vitro in RPMI-1640 containing 1 mg/ml Penicilin/Streptomycin, 1 mg/ml gentamycin, and 1% D-glucose, at 37C and 5% CO2 for up to 72h.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Small RNA libraries were prepared using TriLink small RNA library preparation kit (Illumina compatible), following manufacturer's recommendations.

value: adult

tag: Sex

value: female


title: 48-72h_4


title: Pat8_WM_2_4

description: library of 192 cells


title: LNCaP_CTCF siRNA 144hrs H3K27ac Rep2


title: GKOSM_Day2

city: Tsukuba, Ibaraki

first: Ken

last: Nishimura

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: Gene expression two days after SeVdp(GKOSM) infection

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes followed by hybridization Agilent Whole Mouse Genome Oligo Microarrays for 17 hours at 65°C following the manufacturer's recommendations.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent).

source_name: MEF+SeVdp(GKOSM) Day2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using In-situ oligo DNA microarray kit (Agilent) according to the manufacturer's instructions

extract_protocol: RNA was prepared using the ISOGEN (Nippn Gene) following the manufacturer's recommendations.

treatment_protocol: MEF was infected with SeVdp vector at 32 ºC for a day followed by cultivation in mouse ES cell medium for a day

tag: cell type

value: reprogramming cell


title: miPSC

description: Gene expression in mouse iPSC

source_name: Mouse iPS cells

value: iPS cell


title: LNCaP_CTCF siRNA 144hrs H3K27ac Rep1

value: 20nM CTCF siRNA pool


title: 48-72h_3

tag: developmental stage


title: AG250_3

city: Seoul

first: DONG-MYUNG

last: SHIN

address: Pungnap-2 dong, Songpa-gu

department: Department of Biomedical Sciences

country: South Korea

institute: University of Ulsan College of Medicine

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human 2.0 ST Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC). After importing CEL files, the data were summarized and normalized with *robust multi-average (RMA) method* implemented in Affymetrix Expression Console Software (EC).

label: biotin-labeled with TdT

source_name: Human embryonic stem-cell (H9-hESC)-derived multipotent stem-cells (M-MSCs)

label_protocol: Biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Human embryonic stem-cell (hESC)-derived multipotent stem-cells (M-MSCs) were were cultured with EGM2-MV medium (Lonza, San Diego, CA) on plates coated with rat tail collagen type I (Sigma-Aldrich, St. Louis, MO) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol: Total RNA from various cells was isolated using the RNeasy Mini Kit (QIAGEN, Valencia, CA), including treatment with DNase I (QIAGEN)

treatment_protocol: M-MSCs were maintained in the absence or presence of ascorbic acid 2-glucose (AA2G) of 0.74mM (250 ug/ml) for 3 days

tag: gender

value: Female

tag: tissue

value: inner cell mass

tag: derived from

value: H9 embryonic stem cells

value: Mesenchymal stem cell


title: MEF

description: Gene expression in MEF

source_name: Mouse embryonic fibroblast

value: somatic cell


title: Pat8_WM_1_3

description: library of 192 cells

value: Brain


title: HCT116_MT-1_rep1.

first: YUJIN

last: KWON

address: 50 Yonsei-fo, Seodaemun-gu

institute: YONSEI UNIVERSITY

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: HCT116 cells were maintained in Roswell Park Memorial Institute (RPMI) medium, both containing 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C in a 5% CO2 incubator.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), according to manufacturer instructions.

treatment_protocol: No treatment.

tag: genotype

value: mutant beta-catenin allele


title: AG0_4

description: control replicate#3


title: LNCaP_CTCF siRNA 144hrs H3K4me3 Rep2


title: AG250_2


title: KOSM_Day2

description: Gene expression two days after SeVdp(KOSM) infection

source_name: MEF+SeVdp(KOSM) Day2


title: AG250_1


title: AG0_3

description: control replicate#2


title: Pat8_GM_2_2

description: library of 192 cells

value: Control

value: Temporal lobe


title: 250ug2

data_processing: Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC). After importing CEL files, the data were summarized and normalized with *robust multi-average (RMA) method* implemented in Affymetrix   Expression Console Software (EC).

source_name: murine embryo

growth_protocol: R1 mESCs were grown in 15% heat-inactivated fetal bovine serum (FBS; HyClone, Pittsburgh, PA) and 100 IU/ml ESGRO/LIF (Millipore, Billerica, MA) on a 0.1% gelatin coated tissue culture at 37'C 5% CO2 conditions

treatment_protocol: R1 mESCs were maintained in the abasence (NT) or presence (250ug) of ascorbic acid 2-glucose (AA2G) of 0.74mM (250 ug/ml) for 3 days

value: male

tag: strain

value: embryonic stem cell, R1

value: embryo


title: AG0_2

description: control replicate#1


title: HCT116_WT-1_rep1.

value: wild-type allele


title: 48-72h_1

value: adult

value: female


title: LNCaP_CTCF siRNA 144hrs H3K4me3 Rep1

value: LNCaP Prostate Cancer Cells

tag: chip antibody


title: 250ug1


title: Pat8_GM_1_1

description: library of 192 cells


title: 250ug3


title: Pat7_WM2_MS_Ctrl_2_8

description: library of 192 cells


title: LNCaP_Control siRNA 144hrs CTCF Rep1

value: CTCF

value: 20nM Non-Target siRNA pool

tag: time


title: LNCaP_Control siRNA 144hrs CTCF Rep2


title: NT3

description: control replicate#3

value: inner cell mass


title: HCT116_WT-2_rep2.


title: 0-24h_4

source_name: adult female worms ES products 24h


title: NT2

description: control replicate#2


title: Pat7_WM2_MS_Ctrl_1_7

description: library of 192 cells


title: HCT116_MT-2_rep2.


title: 0-24h_3


title: LC, cKO rep5

city: Rehovot

first: Ayelet

last: Erez

address: 234 Herzl Street

department: Biological Regulation

country: Israel

institute: Weizmann Institute of Science

data_processing:
Fastq files for each sample were generated by the usage of bcl2fastq-v2.17.1.14 software (basecalling)
Reads were trimmed using cutadapt
Reads were aligned to the mouse genome mm10 using, TopHat (v2.0.10).
Counting reads on reference genome, RefSeq release mm10, was done with HTSeq-count (version 0.6.1p1)
Differential analysis was carried out using DESeq2 (1.6.3)
Genome_build: mm10
Supplementary_files_format_and_content: processed1_raw_counts.xlsx
Supplementary_files_format_and_content: processed2_normalized_counts.xlsx

source_name: Locus coeruleus

extract_protocol:
Brains were removed rapidly, embedded and frozen in OCT on dry ice without fixation. 8μm thick sections were cut from the frozen block, mounted on polyethylene membrane-coated glass slides and kept in -80°C. At the day of the experiment, slides were thawed for 5 minutes in room temperature followed by fixation in 70% ethanol (30s), incubation in DEPC water, stained with 150µl 1% crystal violet acetate, and washed vigorously in 100% ethanol for a total of 30s and air dried for 3m before microdissection. Tissue sections were microdissected using a UV laser-based PALM Microbeam.
SMARTer Ultra Low Input RNA followed by in-house DNA Seq protocol

tag: age

value: post natal day 35

value: ASL-LC cKO


title: 48-72h_2


title: 0-24h_2


title: Pat7_WM_2_4

description: library of 192 cells


title: LNCaP_Control siRNA 144hrs H3K27ac Rep1


title: Pat7_WM_1_3

description: library of 192 cells


title: LC, cKO rep4


title: LC, cKO rep3


title: 0-24h_1


title: Pat7_GM_2_2

description: library of 192 cells


title: LNCaP_Control siRNA 144hrs H3K4me3 Rep1


title: LNCaP_Control siRNA 144hrs H3K4me3 Rep2


title: LC, cKO rep2


title: Pat6_Plate2_1_6

description: library of 192 cells


title: 0-24h_5


title: mf_7_ES

source_name: microfilariae ES products

value: microfilariae


title: LC, cKO rep1

value: Brain


title: mf_8_ES


title: Pat6_Plate2_1_5

description: library of 192 cells


title: LNCaP_Control siRNA 144hrs H3K27ac Rep2


title: mf_6_ES


title: LC, WT rep4

value: WT


title: mf_5_ES


title: Pat6_Plate1_2_2

description: library of 192 cells

value: Control